ArticleNucleic acids research2024
HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers, 1 of them a synthesis that pooled it.
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97 citing papers in PubMed, 1 synthesis or guideline pooled it, 128 citations in OpenAlex.
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- Massively parallel characterization and predictive modelling of neuronal regulatory variation.bioRxiv : the preprint server for biology · 2026Article
- FABIAN-variant 2026: improved prediction of the effects of DNA variants on transcription factor binding.Nucleic acids research · 2026Article
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- Decoding common and rare noncoding variant effects across cellular and developmental contexts.Nature genetics · 2026Article
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- Refining sequence-to-expression modelling with chromatin accessibility.Bioinformatics (Oxford, England) · 2026Article
37 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors at 11 institutions in 3 countries.
Funding
Abstract
We present a major update of the HOCOMOCO collection that provides DNA binding specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make this release, we performed motif discovery in peak sets that originated from 14 183 ChIP-Seq experiments and reads from 2554 HT-SELEX experiments yielding more than 400 thousand candidate motifs. The candidate motifs were annotated according to their similarity to known motifs and the hierarchy of DNA-binding domains of the respective transcription factors. Next, the motifs underwent human expert curation to stratify distinct motif subtypes and remove non-informative patterns and common artifacts. Finally, the curated subset of 100 thousand motifs was supplied to the automated benchmarking to select the best-performing motifs for each transcription factor. The resulting HOCOMOCO v12 core collection contains 1443 verified position weight matrices, including distinct subtypes of DNA binding motifs for particular transcription factors. In addition to the core collection, HOCOMOCO v12 provides motif sets optimized for the recognition of binding sites in vivo and in vitro, and for annotation of regulatory sequence variants. HOCOMOCO is available at https://hocomoco12.autosome.org and https://hocomoco.autosome.org.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.